2022
Placing human gene families into their evolutionary context
Dornburg A, Mallik R, Wang Z, Bernal M, Thompson B, Bruford E, Nebert D, Vasiliou V, Yohe L, Yoder J, Townsend J. Placing human gene families into their evolutionary context. Human Genomics 2022, 16: 56. PMID: 36369063, PMCID: PMC9652883, DOI: 10.1186/s40246-022-00429-5.Peer-Reviewed Original ResearchConceptsHuman gene familyGene familyHuman genomeEvolutionary contextGene family evolutionNon-model organismsFirst human genomeGenome biologyComparative genomicsFamily evolutionDistant speciesDraft sequenceGenomic studiesGene expressionGenome sequencingSequence complexityGenomeCancer biologyUnprecedented insightsNovel discoveriesCritical roleOrganismsBiologyComparative approachFamilySecondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa
Wang Z, Lopez-Giraldez F, Slot J, Yarden O, Trail F, Townsend JP. Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa. MSystems 2022, 7: e00232-22. PMID: 35638725, PMCID: PMC9239088, DOI: 10.1128/msystems.00232-22.Peer-Reviewed Original ResearchConceptsSM clustersComparative genomicsSecondary metabolitesAsexual growthN. crassaNeurospora crassaSecondary metabolism gene clustersSexual developmentDevelopmental stagesSecondary metabolite clustersComparative genomic analysisExtensive transcriptomic dataGene expression patternsEnvironmental conditionsFungal toxin productionLevel of RNASMC genesLife cycleRegulatory switchComputational annotationGene clusterEnvironmental signalsMetabolite clustersGenomic analysisKnockout phenotypes
2020
Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification
Dornburg A, Wang Z, Wang J, Mo ES, López-Giráldez F, Townsend JP. Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification. Genome Biology And Evolution 2020, 13: evaa228. PMID: 33196781, PMCID: PMC7851593, DOI: 10.1093/gbe/evaa228.Peer-Reviewed Original ResearchConceptsLeukocyte tyrosine kinaseEvolutionary historyPhylogenetic analysisProtein-coding genesComparative genomic analysisEarly embryonic expressionMetazoan genomesComparative genomicsPhylogenetic contextModel organismsEmbryonic expressionModel speciesHuman genesKey genesGenomic analysisImportant genesMammal systemsFunctional convergenceTyrosine kinaseMolecular homologyGenesFunctional roleVertebratesMammal modelsHomology
2019
Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellum
Kim W, Cavinder B, Proctor RH, O’Donnell K, Townsend JP, Trail F. Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellum. Frontiers In Microbiology 2019, 10: 1247. PMID: 31231336, PMCID: PMC6568001, DOI: 10.3389/fmicb.2019.01247.Peer-Reviewed Original ResearchPolyketide synthase genesPerithecium developmentSynthase geneLife historySecondary metabolite gene clustersDiverse ecological nichesRoot rot pathogensComparative genomicsGene numberPlant pathogensLarger peritheciaGene clusterEcological nichesTransport genesMetabolic potentialGenomic underpinningsTranscriptomic analysisCosmopolitan fungusLarger ascosporesTransporter geneGenomeGenesNovel insightsField cropsSexual development
2004
Gene expression profiling in evolutionary genetics
Hartl D, Meiklejohn C, Castillo-Davis C, Cavalieri D, Ranz J, Townsend J. Gene expression profiling in evolutionary genetics. 2004, 74-93. DOI: 10.1017/cbo9780511542619.007.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsNatural populationsPopulation geneticsKey model organismGenotypes of organismsGene expression profilingDNA sequencing strategyEvolutionary geneticsComparative genomicsEvolutionary timeModel organismsChain termination methodHuman genomePopulation geneticistsGenomic sequencesGenetic variationSingle speciesComplete sequenceExpression profilingMolecular geneticsGenetic differencesGenomeMolecular biologySequencing strategyMolecular levelDNA sequencing